How did skates evolve to develop wing-shaped fins?

Scientists at IRB Barcelona and the Barcelona Supercomputing Center - National Supercomputing Center (BSC-CNS) have participated in a study led by the Andalusian Centre for Developmental Biology (CABD), part of the Spanish National Research Council (CSIC), which has discovered how the skate’s fins evolved by studying its DNA. The work confirms that the key to the development of its characteristic wing shape does not lie in the coding regions of its genome, called genes, but in the non-coding portions and the three-dimensional (3D) complexes in which they fold, called " topologically associated domains" (TAD).

Until now, studies on genome evolution have focused on the coding regions. However, this new work, which has involved groups from Germany, the United States, and the United Kingdom, has described in the journal Nature that the genomic changes that alter TADs can drive evolution. Therefore, the study opens the door to a new way of understanding how genomes evolve structurally and functionally to promote the appearance of new traits.

Skates are one of our most distant vertebrate relatives and they belong to a lineage of cartilaginous fish that also includes sharks. These distant cousins are highly relevant organisms for understanding the evolution of the features that made us human, such as limbs. Performed with the stingray Leucoraja erinacea, the experiments have allowed the researchers to compare the characteristics of these fish with those of other species and to determine what is novel and what is ancestral during evolution.

Involving Dr. Toni Gabaldón, ICREA researcher and leader of the Comparative Genomics group (a joint lab run by the BSC and IRB Barcelona), this new study suggests that the 3D structure of the genome would also participate in the evolution of other interesting traits in certain species that we observe in nature. By combining the study of expression, regulation, and 3D organisation of genes, the field of evolutionary genomics is advancing into a new era of discovery.

“We have observed the evolution of the genome and detected the genes of this type of skate that equate to those of other vertebrates. To this end, we have used databases of sequenced organisms that have allowed us to reconstruct the evolutionary history of all the genes in the genome—a computationally intense process that we have been able to do quickly and efficiently thanks to the MareNostrum supercomputer,” says Dr. Gabaldón.

Reference article:

The little skate genome and the evolutionary emergence of wing-like fins
Ferdinand Marlétaz, Elisa de la Calle-Mustienes, Rafael D. Acemel, Christina Paliou, Silvia Naranjo, Pedro Manuel Martínez-García, Ildefonso Cases, Victoria A. Sleight, Christine Hirschberger, Marina Marcet-Houben, Dina Navon, Ali Andrescavage, Ksenia Skvortsova, Paul Edward Duckett, Álvaro González-Rajal, Ozren Bogdanovic, Johan H. Gibcus, Liyan Yang, Lourdes Gallardo-Fuentes, Ismael Sospedra, Javier Lopez-Rios, Fabrice Darbellay, Axel Visel, Job Dekker, Neil Shubin, Toni Gabaldón, Tetsuya Nakamura, Juan J. Tena, Darío G. Lupiáñez, Daniel S. Rokhsar & José Luis Gómez-Skarmeta
Nature (2023) DOI: 10.1038/s41586-023-05868-1